19-3958897-C-G

Variant names:

• chr19-3958897-C-G
• rs3745982
• NM_001348.3:c.*204G>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001348.3(DAPK3):​c.*204G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DAPK3 NM_001348.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 12 publications found

Genes affected

DAPK3 (HGNC:2676): (death associated protein kinase 3) Death-associated protein kinase 3 (DAPK3) induces morphological changes in apoptosis when overexpressed in mammalian cells. These results suggest that DAPK3 may play a role in the induction of apoptosis. [provided by RefSeq, Jul 2008]

ENSG00000294388 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DAPK3	NM_001348.3	c.*204G>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000545797.7	NP_001339.1
DAPK3	NM_001375658.1	c.*204G>C		3_prime_UTR_variant	Exon 9 of 9		NP_001362587.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DAPK3	ENST00000545797.7	c.*204G>C		3_prime_UTR_variant	Exon 9 of 9	2	NM_001348.3	ENSP00000442973.1
DAPK3	ENST00000301264.7	c.*204G>C		3_prime_UTR_variant	Exon 8 of 8	1		ENSP00000301264.3
DAPK3	ENST00000595279.1	n.1619G>C		non_coding_transcript_exon_variant	Exon 3 of 3	2
ENSG00000294388	ENST00000723280.1	n.1768-1741C>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 3

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		1.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3745982; hg19: chr19-3958895;